Job ID = 2589181 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,379,799 reads read : 4,379,799 reads written : 4,379,799 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107563.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:31 4379799 reads; of these: 4379799 (100.00%) were unpaired; of these: 3295951 (75.25%) aligned 0 times 909859 (20.77%) aligned exactly 1 time 173989 (3.97%) aligned >1 times 24.75% overall alignment rate Time searching: 00:00:31 Overall time: 00:00:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 89409 / 1083848 = 0.0825 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 12 Aug 2019 17:05:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 17:05:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:05:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:05:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 17:05:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:05:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:05:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 17:05:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:05:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:05:28: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:05:28: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:05:28: #1 total tags in treatment: 994439 INFO @ Mon, 12 Aug 2019 17:05:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:05:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:05:28: #1 tags after filtering in treatment: 994439 INFO @ Mon, 12 Aug 2019 17:05:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:05:28: #1 finished! INFO @ Mon, 12 Aug 2019 17:05:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:05:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:05:28: #2 number of paired peaks: 2176 INFO @ Mon, 12 Aug 2019 17:05:28: start model_add_line... INFO @ Mon, 12 Aug 2019 17:05:28: start X-correlation... INFO @ Mon, 12 Aug 2019 17:05:28: end of X-cor INFO @ Mon, 12 Aug 2019 17:05:28: #2 finished! INFO @ Mon, 12 Aug 2019 17:05:28: #2 predicted fragment length is 146 bps INFO @ Mon, 12 Aug 2019 17:05:28: #2 alternative fragment length(s) may be 146 bps INFO @ Mon, 12 Aug 2019 17:05:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.05_model.r INFO @ Mon, 12 Aug 2019 17:05:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:05:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:05:29: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:05:29: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:05:29: #1 total tags in treatment: 994439 INFO @ Mon, 12 Aug 2019 17:05:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:05:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:05:29: #1 tags after filtering in treatment: 994439 INFO @ Mon, 12 Aug 2019 17:05:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:05:29: #1 finished! INFO @ Mon, 12 Aug 2019 17:05:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:05:29: #2 number of paired peaks: 2176 INFO @ Mon, 12 Aug 2019 17:05:29: start model_add_line... INFO @ Mon, 12 Aug 2019 17:05:29: start X-correlation... INFO @ Mon, 12 Aug 2019 17:05:29: end of X-cor INFO @ Mon, 12 Aug 2019 17:05:29: #2 finished! INFO @ Mon, 12 Aug 2019 17:05:29: #2 predicted fragment length is 146 bps INFO @ Mon, 12 Aug 2019 17:05:29: #2 alternative fragment length(s) may be 146 bps INFO @ Mon, 12 Aug 2019 17:05:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.10_model.r INFO @ Mon, 12 Aug 2019 17:05:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:05:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:05:30: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:05:30: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:05:30: #1 total tags in treatment: 994439 INFO @ Mon, 12 Aug 2019 17:05:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:05:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:05:30: #1 tags after filtering in treatment: 994439 INFO @ Mon, 12 Aug 2019 17:05:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:05:30: #1 finished! INFO @ Mon, 12 Aug 2019 17:05:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:05:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:05:30: #2 number of paired peaks: 2176 INFO @ Mon, 12 Aug 2019 17:05:30: start model_add_line... INFO @ Mon, 12 Aug 2019 17:05:30: start X-correlation... INFO @ Mon, 12 Aug 2019 17:05:30: end of X-cor INFO @ Mon, 12 Aug 2019 17:05:30: #2 finished! INFO @ Mon, 12 Aug 2019 17:05:30: #2 predicted fragment length is 146 bps INFO @ Mon, 12 Aug 2019 17:05:30: #2 alternative fragment length(s) may be 146 bps INFO @ Mon, 12 Aug 2019 17:05:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.20_model.r INFO @ Mon, 12 Aug 2019 17:05:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:05:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:05:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:05:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:05:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:05:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:05:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.05_summits.bed INFO @ Mon, 12 Aug 2019 17:05:33: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2495 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:05:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:05:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:05:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:05:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.10_summits.bed INFO @ Mon, 12 Aug 2019 17:05:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1517 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:05:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:05:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:05:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043988/SRX043988.20_summits.bed INFO @ Mon, 12 Aug 2019 17:05:35: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (726 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。